GATK VQSR for human WGS

0

Hello all,

I'm working with human WGS data from germline for rare disease.

I'm a bit lost for the VQSR step because the command (option) are not the same between the tool page and the tuto page.

I don't really understand the differences i use the option --tranches or not.

Maybe someone could give me a good "classic" method for these type of human data? Or maybe just used the default parameters ?

Thanks in advance


WGS


alignment


genome

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